Porter, M. L., T. Cronin, D. A. McClellan, and K. A. Crandall.  "Molecular characterization of crustacean visual pigments and the evolution of pancrustacean opsins."  Molecular Biology and Evolution.  24 (2007): 253-268. 

Perez-Losada, M., R. G. Christensen, D. A. McClellan, B. J. Adams, R. P. Viscidi, and K. A. Crandall.  "Comparing phylogenetic codivergence between polyomaviruses and their hosts."  Journal of Virology.  80 (2006): 5663-5669. 

Ebbert, M. T. W., T. D. O'Connor, W. A. Beckstead, M. J. Clement, and D. A. McClellan.  "Pharmacogenomics: Analyzing SNPs in the CYP2D6 gene using amino acid properties."  Proceedings of the Biotechnology and Bioinformatics Symposium.  3 (2006): 1-5. 

Baer, K. and D. A. McClellan.  "Molecular coevolution of the vertebrate cytochrome c1 and Rieske iron sulfer proteins in the cytochrome bc1 complex."  Proceedings of the Biotechnology and Bioinformatics Symposium.  3 (2006): 10-18. 

Chamala, S., W. A. Beckstead, M. J. Rowe, and D. A. McClellan.  "Evolutionary selective pressure on three mitochondrial SNPs is consistent with their influence on metabolic efficiency in Pima Indians."  Proceedings of the Biotechnology and Bioinformatics Symposium.  3 (2006): 35-44. 

Smith, R. L., S. A. Loughmiller, and D. A. McClellan.  "Analysis of the effects of positive selection on physicochemical properties in the nicotinic acetylcholine receptor and associated structural implications."  Proceedings of the Biotechnology and Bioinformatics Symposium.  3 (2006): 112-115. 

Porter, M. L., T. W. Cronin, D. A. McClellan, and K. A. Crandall.  "The molecular evolution of invertebrate opsins."  Investigative Ophthalmology & Visual Science.  47.E-Abstract (2006): 3748. 

A. C. Edmondson, D. Song, L. A. Alvarez, M. K. Wall, D. Almond, DAVID A. McCLELLAN, A. Maxwell, and B. L. Nielsen.  "Characterization of an Arabidopsis thaliana mitochondrial-targeted single-stranded DNA binding protein."  Molecular and General Genomics.  273 (2005): 115-122. 

DAVID A. McCLELLAN, J. L. Moss, E. J. Palfreyman, M. J. Smith, R. G. Christensen, and J. K. Sailsbery.  "Physicochemical evolution and molecular adaptation of the cetacean cytochrome b protein."  Molecular Biology and Evolution.  22 (2005): 437-455. 

McClellan, D. A., D. F. Whiting, R. G. Christensen, and J. K. Sailsbery.  "Genetic codes as evolutionary filters: Subtle differences in the structures of genetic codes result in significant differences in patterns of nucleotide substitution."  Journal of Theoretical Biology.  226:393-400 (2004). 

Wooley, S., M. Smith, J. Johnson, D. A. McClellan, K. A. Crandall.  "Tree SAAP: Selection on Amino Acid Properties using phylogenetic trees."  Bioinformatics.  19 (2003): 671-672. 

DAVID A. McCLELLAN.  "Detecting Lehi's genetic signature."  FARMS Review.  15 (2003): 35-90. 

McClellan, D. A. and K. G. McCracken.  "Estimating the influence of selection on the variable amino acid sites of the cytochrome b protein functional domains."  Molecular Biology and Evolution.  18 (2001): 917-925. 

McClellan, D. A.  "The codon-degeneracy model of molecular evolution."  Journal of Molecular Evolution.  50 (2000): 131-140. 

McClellan, D. A.  "The phylogenetic utility of the codon-degeneracy model."  Journal of Molecular Evolution.  51 (2000): 185-193. 

McCracken, K. G., J. Harshman, D. A. McClellan, and A. D. Afton.  "Data set incongruence and correlated character evolution: an example of functional convergence in the hind-limbs of stifftail diving ducks."  Systematic Biology.  48 (1999): 36-68. 

M. Perez-Losada, DAVID A. McCLELLAN, R. G. Christensen, R. P. Viscidi, and K. A. Crandall.  Phylogenomics and molecular evolution of polyomaviruses. In: Polyomavirus and Human Diseases.  Ed. N. Ahsan.  1st ed.  Georgetown, Texas: Landes Bioscience, Mar. 2005.